Use scores to get ordination scores: summary.cca will fail in the next release

[jarioksa]

Next vegan release will drop ordination scores from the summary.cca result object. You should use scores function instead. The reason for this change is that summary did not fulfil its task to provide a summary: it spat out huge volumes of scores and hid the summary part. This was a long-standing issue with developers raised in 2016 in issue #203. The fix is easy: use scores() function instead of summary(). Some simple rules of changes:

• In simple use cases you can just change the function name: summary(foo)$sites → scores(foo)$sites plus add importFrom(vegan, scores) in your NAMESPACE (if you use that).
• scores function is configurable, and more complicated cases are better specified with arguments: summary(foo)$sites[, 1] → scores(foo, display = "sites", choices = 1).
• scores knows same argument as summary, and in many cases you do not need to change those with the change. There is one important exception: summary had argument axes that gives the number of returned axes from the beginning, but scores has argument choices that is a vector of axis numbers. So you should change axes = n → choices = seq_len(n). With choices you can also skip some axes and you do not need to start from axis 1.
• summary.cca defaulted to six axes, scores defaults to two axes. It is best to define the number of axes explicitly with choices.

The current release candidate uses old summary.cca to get scores (but will not print them). This gives a grace period to change your package, and you may not yet see the change. This is a temporary relief which is only made in the current release branch (2.6-6), and later releases will require using scores to get scores.